Mercurial > repos > iuc > imagej2_bunwarpj_align

annotate jython_script.py @ 0:7a96d686d380 draft

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planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
author iuc
date Tue, 09 Jun 2015 12:22:23 -0400
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children be709f819445
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7a96d686d380 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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1 import sys
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2 import imagej2_base_utils
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3 from ij import IJ
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4
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5 # Fiji Jython interpreter implements Python 2.5 which does not
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6 # provide support for argparse.
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7
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8 if sys.argv[ -1 ].lower() in [ 'true' ]:
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9 mono = True
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10 else:
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11 mono = False
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12
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13 if mono:
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14 # bUnwarpJ has been called with the -mono param.
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15 source_tiff_path = sys.argv[ -4 ]
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16 source_datatype = sys.argv[ -3 ]
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17 source_path = sys.argv[ -2 ]
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18 else:
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19 source_tiff_path = sys.argv[ -7 ]
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20 source_datatype = sys.argv[ -6 ]
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21 source_path = sys.argv[ -5 ]
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22 target_tiff_path = sys.argv[ -4 ]
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23 target_datatype = sys.argv[ -3 ]
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24 target_path = sys.argv[ -2 ]
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25
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26 def convert_before_saving_as_tiff( registered_image ):
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27 # The bUnwarpJ macro produces tiff image stacks consisting of 3
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28 # slices which can be viewed in ImageJ. The 3 slices are::
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29 # 1) the registered image, 2) the target image and 3) the black/white
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30 # warp image. Galaxy supports only single-layered images, so we have
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31 # to convert the image to something other than tiff so that slices are
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32 # eliminated and we can then convert back to tiff for saving. This is
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33 # kind of a hack - there is probably a way to do this without converting
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34 # twice. I messed around with the the ImageJ getSlice() method, but
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35 # couldn't get it to produce what is needed here.
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36 tmp_dir = imagej2_base_utils.get_temp_dir()
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37 tmp_out_png_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'png' )
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38 IJ.saveAs( registered_image, 'png', tmp_out_png_path )
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39 return IJ.openImage( tmp_out_png_path )
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40
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41 # Save the Registered Source Image.
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42 registered_source_image = IJ.openImage( source_tiff_path )
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43 if source_datatype == 'tiff':
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44 registered_source_image = convert_before_saving_as_tiff( registered_source_image )
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45 IJ.saveAs( registered_source_image, source_datatype, source_path )
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46
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47 if not mono:
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48 # Save the Registered Target Image.
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49 registered_target_image = IJ.openImage( target_tiff_path )
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50 if target_datatype == 'tiff':
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51 registered_target_image = convert_before_saving_as_tiff( registered_target_image )
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52 IJ.saveAs( registered_target_image, target_datatype, target_path )